We have recently developed a prototype system for long-term monitoring of single-cell behaviors in complex tissues. Our system comes from the synergistic integration and optimization of two leading technologies in microscopy and computational cell tracking: the inverted selective plane illumination microscope (iSPIM) and the StarryNite software package. We have demonstrated order-of-magnitude improvements on virtually all fronts compared to the standard technologies in use, notably imaging speed, reduction of phototoxicity, accuracy of cell tracking, and lower demand for computing power, all achieved at a reduced cost with comparable or better image quality. Our system has been applied to multiple model organisms as well as cell culture, demonstrating its versatility. We aim to bring the system to maturity and into the hands of the research community as a powerful and versatile tool for single-cell studies in complex, differentiating cell populations.